Metroid Revolution
by Arch-Fire
Summary: Samus is evading capture from the Federation. To her, the situation seems simple. In reality it's very complicated. Space Pirates, The Federation, the Chozo and many other parties are involved, so Samus has a lot of work to do. Set after Metroid Fusion.
1. Plight of a Fallen Hero

**Pre-Story Notes**

**Yeah, I know this stuff is horrendously boring and tedious but I felt I had to add this. In writing this fan-fic, I have tried to make sure that fans who may have missed a few games or plot elements can understand it, in case you're wondering why I stop to clarify some things here and there, and this will happen less and less as the story goes on. Also, any feedback or criticism would be appreciated, as this is my first real attempt at a proper fan-fic, so if something doesn't make sense or something like that just let me know. **

It had been three months since any major events regarding the war between the Space Pirates and the Galactic Federation had occurred. The uneducated person's judgement would think that a ceasefire was in effect, or even that the galaxy was at peace again, for the first time in years. The Space Pirates had been held back to their homeworld, unseen, and no rumours of criminal activities were circulating to suggest that the Space Pirates were concocting another 'evil scheme.' Even Galactic Federation hadn't released any details to the public about their operations, if there were any at all. Some uninformed leaders were labelling it "The Make-Believe War", and some citizens were questioning the Federation's capacity to lead the galaxy.

However, both the Space Pirates and the Galactic Federation were secretly after one thing, irrelevant to the public perception of the Federation, and also something not directly relevant to wiping out the other power. This thing, however, could threaten to undermine both of them unless it was eliminated quickly. In fact, this thing was currently trying to evade detection from them in the far reaches of space, far from Federation and Pirate Settlements.

.******

Meanwhile, a purple gunship drifted by an unknown star system. The sleek, streamlined Hunter-Class Ship, of Federation technology had powerful, state-of-the-art weaponry and defences and was capable of some spectacular aerial manoeuvres to avoid taking damage. Inside was a fugitive, Samus Aran.

Samus was both physically, and mentally, adrift. Her thick, expressionless Power Suit, of Chozo origin with Federation modifications , belied the deep feelings of worry she felt. Her betrayal of the sole ally she had may be something she would not live to regret. They were after her, and she knew it. Samus lay still in her ship, thinking. Should she hand herself over, or continue on evading with the impossible hope of avoiding capture. What would happen if she was captured? Where could she land to refuel? These are the questions she had pondered over endlessly during the past three months, and this could've continued for another three if she wasn't interrupted.

"The Galactic Federation has sent a message, lady." called the voice of Samus' on board computer.

That computer served her well in the past; the voice and personality of her former Commanding Officer Adam Malkovich, who gave up his life to save Samus on one of her missions, always encouraged and reassured her when she needed it, and Samus always referred to it as 'Adam' because of this.

"Listen to it yourself." continued the computer.

A transmission came through on the ship's radio.

"Samus, this is the High Admiral of this sector of the Federation." declared an unidentifiable male voice. "This your final warning to turn yourself in to the nearest Federation ship, the G.F.S. Olympus, to stand trial, or we will be forced to bring you in by force. Repeat, this is your final warning  to turn yourself in."

Samus knew instantly that the Federation had found her. Her metal clad feet rose from her leather chair and paced up and down the cockpit as she pondered her fate. She knew that the Federation would not go easy on her on trial. They wanted the contents of that ship, and she had directly prevented them from having it, then ran from judge's for 3 months. If there was one thing Samus knew about the Galactic Federation, it was that if something stood in their way, they would stop at nothing to neutralise the threat. It was this reasoning that made her run in the first place, and it would be this reasoning that would make her continue to run, despite the hopelessness of the task at hand.

******

The G.F.S. Olympus was a massive vessel, pride of the Federation's Fleets. The ship had many docking bays for ships to land, as well as a heavily guarded command bridge housing many Fleet Admirals, as well as a singular High Admiral that as the difficult job of controlling the ship as well as the many Federation troops, ships and computer systems. The ship was heavily armed and defended, and fought off a Space Pirate attack once before as part of an assault on some of the main planets controlled by the Federation. If one thing was certain, it was that the Olympus would not fall easily.

Inside its intricate hallways and rooms, the High Admiral waited for news about Samus Aran's response to their repeated demands.

"Has Samus arrived abroad the ship." the High Admiral asked a trooper.

"Not yet, Sir" came the troopers reply.

"I see..." the Admiral paused for thought "She has had more than enough time to consider our demands. We must intercept her before she can get away again."

"May I recommended the new model of Federation Bombers, Sir." said the trooper sarcastically.

"No, I have a better idea" declared the High Admiral. "We'll use the full force of the ship against her. Full power to the engines." the Admiral yelled. "We are going to get her on board this ship no matter how or what!"

******

Samus felt increasingly nervous as she continued to cruise through unknown areas. The Federation had no doubt sent a force to capture them now, and Samus had to prepare.

"Adam, activate the radar," Samus ordered "we need the locations of all nearby ships."

"As you command, Samus." Adam replied.

Samus waited patiently, despite the circumstances, until Adam had a result. She admired her Fusion Suit, a combination of Chozo, the race that raised Samus and Federation Technology, and marvelled at the Metroid DNA that saved her life, but leaving her vulnerable to cold. Samus had been feeling very sentimental recently, though three months with nothing but a computer for company would do that.

"Samus, bad news." said Adam coldly, his computerised voice not appreciating the magnitude of the situation. "My scans have revealed two craft in the area. One is a Space Pirate probe, and it has been tracking us, as well as the Olympus. Speaking of the Olympus, it is now in a perfect position to intercept us, is in vacuum torpedo strike range and, should we turn back, they will most likely send fighters after us. We are trapped!"

Samus didn't respond for a moment, her look of shock disguised by her helmet.

"Full power to the shields." Samus ordered. "They have us now."

**Chapter Two will be here sometime next week by the way. Prepare for an OC and a familiar face appearing as the Space Pirates enter the fray. Thanks to PY687 and Woodsballer for pointing out some of my mistakes, by the way.**


	2. The Search Ends

Samus slowly piloted her ship towards the Olympus, hoping desperately not to see or hear weapons-fire from the immense ship as Adam sent the transmission informing of her intention to land aboard the ship. Samus had made the split-second decision that she was tired of running, and that the risks were too great, even for a talented and reckless pilot like her.

"Proceed to Docking Bay 7, Samus Aran. Any escape to escape and you will be fired upon."

Samus was hunched over the controls, making sure she didn't accidently make a sudden move. Samus never would've guessed that she would be doing this a year, or even 6 months ago. She continued to fly towards the ship, eventually reaching the Docking Bay.

The ship landed precisely in the middle of the Landing Pad using its advanced technology. The gunship's four landing 'legs' split apart, and Samus gracefully descended down her ship's tractor beam, and Samus stood on ground other than her ships for the first time in 3 months. Samus had been here before, both before and after she was corrupted with a radioactive mutagen called Phazon. Some troopers radioed something inaudible, and walked towards Samus. Samus noted that their grey suits were more heavily armoured than the typical Federation trooper. It was just like the Federation to take every precaution possible to achieve goals. Some would call it overkill, but the Federation would sooner say 'Better safe than sorry.' The troopers approached Samus, guns raised, though only set to stun.

"Samus Aran," started the trooper moving behind Samus "Follow us. Any attempt at escape and be will fire at you."

The other trooper stood in front to lead a path. This was another precautionary measure taken by the Federation, it was clear they no longer trusted her at all. While that was to be expected, Samus didn't expect two threats like the ones she received. Samus was being led through paths of the ship she had never been before. She became suspicious of what was going to happen; she saw very few troopers, and she could have sworn she saw a prisoner. Samus took a moment to think about the Space Pirate Probe she saw; the Space Pirates knew where she was, maybe the Federation wanted to keep her from defecting to the Space Pirates. After what felt like hours of walking, the two troopers stooped before a door.

"Remove your suit." one of them ordered. Samus didn't respond.

"Remove your suit, or we will use force! Then step inside!"

Samus reluctantly disengaged her suit, by completing a matter to energy reaction, a technology unique to Chozo creations. Her suit was now nothing but energy around her. Samus, now positive that she was going to be imprisoned, stepped inside the room, and looked around. Samus glared at the two troopers from behind her visor, as the door sealed behind her. Samus looked around, scouring the room for windows in the pale blue light. She found nothing, and it was then she realised what was really happening. Samus clutched her head has the pains began. She felt dizzy, and fell to the ground in pain. Samus futily hung on to what consciousness she had left as the fumes entered the room. Slowly, but surely, Samus blacked out.

******

"Our probe tracking Samus Aran has brought some bad news chief." came a harsh voice from the end of the seemingly organic room.

"What would that bad news be." a deep, imposing voice responded.

"Samus Aran has been captured, sir." the voice revealed nervously.

"Incompetent failure!" yelled the second voice.

"I'm sorry, Vulcan, I mean Sir." the voice was panicked now.

"Not good enough!" the voice of Vulcan, a Space Pirate Commander screamed intensely. "You...have failed me...for the last time!"

Vulcan charged swiftly at his 'victim', injecting his poison into the whimpering Space Pirate's cowering body. He fell to the ground in a lifeless heap. Vulcan walked over to another Pirate in the room, still fuming.

"Lets hope you can do a better job than your predecessor." Vulcan said "For your sake. Now, your first order of duty is to bring me Kraid. You can do that, can't you."

"Uh-"

"Don't answer. Now GO!" Vulcan demanded. Vulcan waited for his new 'assistant' to leave the room. "Samus must be captured. We failed three months ago and we will fail now unless I take some action." Vulcan soliloquised "Our plan will not succeed without her."

Vulcan was a tall, muscular Pirate renown for his awesome speed and agility as much as his ruthless leadership. Vulcan had a short temper, and his favourite way of disposing of poor troopers or Pirates that let him down would be to poison them with his deadly venom or transplanted organic 'upgrades' he uses to make himself more powerful. Minutes passed, and eventually, Kraid arrived. Kraid was considerably smaller than in Samus' previous encounters with him, and minus the protrusions on his back and stomach. As a result of his two previous failures against Samus, Kraid had been considerably demoted.

"You sent for me, master." Kraid's crackly, influent voice said.

"Yes, I did." answered Vulcan, finally calming down. "You are to lead an invasion force on to the Galactic Federation Ship Olympus. Your objective is to capture Samus Aran alive at all costs. Do you unterstand?

"Yes, Sir." Kraid answered. Despite Vulcan's vague commands, Kraid knew what he had to do, though even if he didn't understand, he wouldn't dare make Vulcan repeat himself.

"Kraid, make sure you don't fail." Vulcan said "Samus is vital to our mission."

"Sure thing, Sir." Kraid responded assuringly as he left into the acid rain outdoor environment of the Space Pirate Homeworld, known as 'Utragia' to the Pirates. Kraid knew that it was hard a task, however, though his self-confidence was low. He wasn't even close to full power; he was only roughly twice the size of a human Samus' height, and lacking many of the things that originally made him so formiddable. In spite of this, Kraid must try his best to succeed, as Vulcan's wrath exceeds any suffering than death could possibly bring.

**What will happen to Samus? Why is Kraid only at a fraction of his maximum power? The answers to these questions and more, when Chapter 3 comes later this week.**


	3. Trial and Error

**Here's a Christmas present. Two chapters in one day! These were originally one chapter, but I split it in two for the sake of consistency.  
**

"Bring her in." called the voice of the High Admiral.

Samus felt like her head had been crushed under the weight of one thousand star cruisers as her motionless body was dragged into the room. Samus regained control of herself, and slowly pulled herself to her feet, still attempting to identify the faces surrounding her. This room was vaguely familiar to her, yet her half-conscious mind couldn't quite tell exactly where she was.

"Samus Aran" came the High Admiral's voice "You have been charged with directly disobeying top-priority orders and destroying Federation property. Of course, you obviously understand the magnitude of such crimes, because you fled from us for three months."

Samus' mind was recovering steadily, and now she could finally put a name to the High Admiral's voice. It belonged to Jonathan Baxter, the personality equipped to Samus' ship before Adam was. Samus knew that Baxter was a man that doesn't believe in disobeying orders, and came down on anyone that did harshly. He cared nothing about circumstance either, a crime was a just a crime to him. Samus may have saved the galaxy by disobeying orders, but she doubted Baxter would care.

"So, why did you do it?" Baxter asked."Your ship sent a message before you changed the personality suggesting that you thought we couldn't handle the X. You said they could have wiped the entire cosmos had they have survived. We were prepared, Samus. Don't you trust the Federation?"

Samus knew that this was a lie, they weren't prepared at all, otherwise some survivors would be onboard the ship she found them on, with the X in control, but she wouldn't dare challenge Baxter, for fear of digging herself into a deeper hole; she knew she wouldn't be treated fairly, they never even asked how she pleaded. Still, Baxter was already chipping away at Samus' patience.

"Samus, for all we know, you could have been trying to ruin our research so you could try to eliminate us without the X assisting us." Baxter declared.

The X were a parasitic organism Samus destroyed abroad a Federation Research Ship, called the B.S.L. Laboratories to stop them killing the population by infecting their central nervous system, which they take control of. Samus was a victim of X-Infection too. The Federation had removed some of her suit in attempt to save her, leaving her with the 'Fusion Suit'. This failed, though she was saved by a Metroid Vaccine from what she thought to be the last Metroid in existence. The Federation had kept in a Restricted Lab, which an X mimicking her Power Suit had jettisoned .

This suggestion marked the last straw of Samus' patience. "Outrageous!" she yelled at the top of her voice. "I'm a Bounty Hunter, I don't have to follow orders."

This was a landmark occasion, Samus had rarely spoken to anyone other than her ship before.

"On the defensive now, are we." Baxter continued "Some could take that as a sign of guilt. And besides, we hired you to take our orders, you can't just go back on a contract."

Samus stopped, defeated. Baxter had her where he wanted her.

"The Federation is lenient, however. Look at your suit, Samus." Baxter instructed.

Samus saw her suit. The unmistakable grey colour was all she needed to tell what the Federation had done.

"A Standard Federation Suit?" Samus asked, almost in disgust.

"Yes," Baxter replied "You'll be joining the Galactic Federation Army."

Samus took a moment to ponder this sentence. She tried not to think of the word demoted, the thought of it made her cringe.

"This version of the Federation Armour Suit is compatible with your Chozo upgrades, so we can provide them to you if a situation gets desperate. By the way, your suit looks just the same as it did before, just with a different colour and weapons."

Samus was relieved to hear that as she dwelled on what had just occurred. Many questions racked her brain. How had the Federation taken her old suit? Why did they send her to the army? Samus was so busy thinking that she missed Baxter's panicked assistant rush into the room.

"Sir. The sensors in the Command Bridge have detected several Space Pirate ships heading in our direction. The hits show a full size invasion force!" he quickly blurted out.

Samus' attention turned from herself for a moment, hearing Baxter's Assistant's words.

"Samus," Baxter called. "You will go to the Docking Bay you landed on when you were first here, and join Federation Defensive Tactical Unit 2, or FDTU2, to fight off the Pirates. I trust you'll find your way there without any trouble. Is that clear."

Samus didn't bother to give Baxter the satisfaction of an answer, and left the room. Samus walked through the blue door of the Admirals Trial Room into the Command Bridge, a place she had been before when she was first here. Samus had met Fleet Admiral Castor Dane, who was put in charge of her mission at the time. Speaking of Dane, Samus had not seen him in the trial, and wondered about his fate with the Federation; Fleet Admiral was a very dangerous job at times.

Still, Samus had more important things to worry about. She thought about the trial, realising how Baxter had the affair finished with so quickly. She thought that Baxter probably planned the whole thing, just waiting until she would snap, and left herself in a position where she would have to take whatever she received in the way of punishment, without argument. Baxter then sent her to the army so she didn't defect to the Space Pirates, and took her suit away so she couldn't escape. Samus hated being played like that.

Samus then turned to how they had removed her suit when it was only energy around. Only the Chozo training her as a teenager had ever been able to do such a thing. Then, it hit her. The Galactic Federation had figured out how to manipulate things beyond physical existence. Samus shuddered thinking of what the current, reckless leadership could do with it. That would jeopardise the entire galaxy.

Baxter's voice came over the loud speaker. "All men to battle stations, we are under attack from Space Pirates, repeat, we are under attack."

Samus thought to herself that Baxter had something elaborate planned, but what.

******

Baxter reclined in his comfortable office chair. "That went faster than we had planned," he said to his assistant. "Samus cracked so easily. Have we melted Samus' ship down?"

"It's halfway through the queue, sir. One thing , do you reckon the Space Pirates will defeat her?" asked the assistant.

"I think Samus is very capable." Baxter responded. "She will have no trouble against a few measly Pirates."

"I wouldn't be so sure," debated the assistant "Samus' armour won't last long, and the Pirates may focus their fire on her, they're sworn enemies. Still, we'll just have to wait and see. Samus did make an excellent test subject though, wouldn't you agree?"

"Yes, she did." Baxter agreed. "I think her energy Power Suit was a great first test. We collected the energy successfully, and transferred it beyond the physical world. How simple. What's more, all we need to do now is figure out the matter- to-energy formula and we will be able to take control of everything beyond physical existance. The revolution is closer than ever before."


	4. Defence of the Olympus

Samus walked through to the Docking Bay, catching her first glimpse of FDTU2, standing prepared behind a barricade just before the Landing Pad. The room fell silent as she walked in; all eyes were on her. Samus could heard the murmuring voices of the Federation troops speculating about the rumours they had heard about what Samus had done. Disgusted, Samus ignored the voices, and spotted a Space Pirate Landing Ship headed to the Docking Bay.

The Federation troops had spotted it too, and leapt over the barricade to greet it. Samus followed after them, keen to kill as many pirates as possible, the fact that they killed her parents fuelling her desire for revenge. The ship broke through the turret defences, and successfully landed on the Landing Pad. Space Pirates streamed out of the open door, and Samus shot them down as she saw them, bringing on a great feeling of satisfaction. The other troopers who left the barricade weren't faring so well, however. They were falling like dominoes as reinforcements poured out from the protection of the barricade.

Samus spotted a Pirate using a radio; she shot it down with a few headshots from her Power Beam, then turned to dodge the fire from the other pirates. The Landing Ship took off for the transports to pick up more Pirates; Samus quickly fired a missile towards the ship's engine, striking the target directly. The ship exploded spectacularly as Samus took several Federation troopers behind a small, retractable, metal sheet used for cover in these situations. Samus watched from here as the burning remains of the ship took out a large group of Pirates, with shrapnel striking many more down, including a few Federation troops who didn't think to take cover.

Samus strafed out from her cover as the last of the Federation troops emerged from the barricade. Samus released a volley of shots at the Space Pirates, who were still disoriented by the smoke shrouding the area near the Landing Pad. Most of the Pirates were taken down, except one, which fired a series of shots against the few remaining Federation troops. Samus pushed one out of the away, as the shots killed troops all around her. Samus eyed the Pirate through the now clearing smokescreen, evading the shots as she prepared to unleash several shots at its head. Samus was struck in the head by one of the bullets the pirate was spraying around her, her HUD displaying a major loss of energy units from the sole tank she had. Astonished, she fired a string of shots at the Pirates head, swiftly killing it.

Samus saw the levitating Large Energy Unit the last Space Pirate had dropped through the now clear Docking Bay; she promptly collected it, bringing her energy levels back to maximum capacity. Samus checked behind her for any surviving troops, seeing only one, the trooper she pushed out of the way before.

"Thanks...Samus." called the trooper. His cracked visor's light flashed as he spoke and clamoured to his feet.

Samus directed him away from the dock and behind the barricade; if there were any more Space Pirate waves to come, Samus wanted to face them herself.

******

The Space Pirate Cruiser drifted far from the Olympus, holding the Space Pirate leading the operation.

"Have we located Samus Aran yet?" Kraid's low-pitched voice asked impatiently.

" No, not just yet." answered the hoarse voice of a Space Pirate in front of a large computer system. "No- wait a second!" the voice said excitedly "Incoming transmission from aboard the Olympus." The Pirate listened to the transmission carefully.

"The forces at Docking Bay Target 3 have located Samus there." the Pirate stated.

"Good work." Kraid said, moving towards a Landing Ship. "Vulcan will be most satisfied when be bring her back." Kraid stepped into the cockpit. "Make sure you wait for me below the Docking Bay."

******

Samus had waited for quite a while for another wave of Space Pirates to attack. They hadn't arrived, and Samus was considering leaving her post, even though it was against her orders. Then again, who was Samus to follow orders. As she was about to leave, she saw another Landing Ship approaching. It weaved its way through a hail of turret fire and speedily flew into the Docking Bay. Samus readied her Arm Cannon as the ship landed on the Landing Pad. Samus expected an onslaught of Space Pirates, but instead, a tall, grotesque creature walked out.

"Samus." said Kraid as his ship flew away. "I must bring you back to the homeworld...at all costs!"

With those words, Kraid lunged at Samus from across the room. Samus rolled aside, switching to her Scan Visor in the process. As Kraid regrouped for another attempt, Samus began to scan it. Samus stepped around Kraid as he tried to charge into her again, and the scan then completed. Samus quickly checked her logbook and discovered that it had been wiped. Still, she checked Kraid's new entry:

_Kraid_

_A High-Ranking Space Pirate defeated twice before on Zebes. Kraid is considerably smaller than in previous encounters. Body analysis suggests that Kraid has not yet reached maturity, and in-depth cell analysis suggests that all cells are derived from one stem-cell, determining that Kraid originated from cloning. As Kraid is not yet mature, it can only attack by ramming targets. Threat level moderate._

Samus was shocked; the Space Pirates had perfected their cloning technology. They had tried before to clone Metroids, but failed, instead ending up with Mochtroids, Metroids that couldn't attach onto their prey, making them essentially useless. This was a major development.

Kraid launched another attack as Samus switched to her Combat Visor and fired several shots at his head. Kraid tripped and fell after missing Samus as she dived to her right, allowing her to get a charged shot into his belly. Kraid rose to his feet, enraged, and dashed head on towards Samus. Samus dodged this by jumping over Kraid's lowered head. Kraid overshot Samus' position and stopped just before the edge of the Docking Bay. This gave Samus an idea. She backed away from Kraid, shooting as his head and halting just before the edge. Samus baited Kraid lowering her weapon, and Kraid instantly ran at Samus, who jumped of out the way. Kraid just managed to stay on the Docking Bay, teetering precariously on the rim.

Samus delivered a swift kick to Kraid, who plummeted down to space. Samus turned away, awaiting further command, missing Kraid being collected by the ship he told to wait for him earlier. Samus looked out from the Docking Bay as a Space Pirate ship was blown up by defensive turrets. From behind the wreckage, a familiar purple gunship headed towards the Docking Bay...

**Merry Christmas to all, (Even if you don't celebrate it, you still deserve to be happy, right?) and Chapter 5 will come between Christmas and the New Year. **


	5. A New World

Samus was amazed as her ship flew into the Docking Bay. As it flew in, Samus thought about going on the run again. Anything would beat slaving over various military operators for the rest of her capable life. It would be a big risk though; Samus could be punished further, possibly sent to prison. The ship landed, and Samus made the split second decision that serving in the Federation Military was effectively prison with hard labour anyway, and that regular prison would almost be better. Samus didn't really believe this, she just wanted an excuse to be free again. She was pulled into her ship, looking around to detect any possible thieves that may have taken the ship.

"Greetings, Lady." Adam said as the auto-pilot took the ship outside of the Olympus. "We have a lot to talk about. I was told what they had done to you, and what they intended to do, so I was taken and sent here."

"Someone sent you here. Federation Trooper or Pirate?" Samus asked.

"A Federation Trooper. He didn't reveal his name. He released the ship from a line to a melting plant. He said that you were essential to stopping the revolution." Adam replied.

"The revolution?" Samus queried.

"The Federation plan to control the world beyond physical existence, Samus."

Samus thought that she should have figured that Adam meant that. Still, she was happy her theory was all but confirmed now. She thought about what Adam had said before. There was a mole in the Federation assisting her, and this person knew something she didn't.

"What to do about the High Admiral?" Samus said. "If he plans to use the world beyond physical existence to control us we need to stop him."

"Samus, first, I recommend that our first priority is that you focus your attention on upgrading your suit" Adam suggested. "You can't take on any revolution with just the Power Beam and five downgraded Missiles. Where do you want to travel to?"

" Set a course for Tallon IV." Samus commanded. "The Chozo Ruins there should be laden with upgrades."

"Engaging Hyperdrive." Adam stated. "Destination, Tallon IV." The ship took off, and Samus had escaped the Federation's grasp once again.

******

"Check the status of the ship's shields." Baxter ordered from his control station.

"Half capacity." his assistant replied from his station. "Space Pirate Boarding Pods have breached the ship near our Communications Bay. Troops have successfully fought them off, though."

"How about the status of our troops?" Baxter asked.

"Reinforcements are depleted in the Production Bay, as well as Docking Bays Three, Six, Eight and Eleven. Our defence turrets are mostly intact, except near most of the Docking Bays." the assistant answered.

"Hang on, did you say Docking Bay Three?" Baxter asked rhetorically. "Samus is stationed there. Looks like you were right, Samus didn't last two hours. She is now just one more thing we don't have to worry about."

Baxter's assistant peered out of the window, carefully analysing the fighters battling outside. His eyes were fixed on one particular ship that had taken out several Space Pirate Fighters consecutively. It swerved around a Space Pirate Bomber and delivered heavy fire to the ship, which exploded violently and sent wreckage careening into other Pirate ships, destroying them too. The ship flew by the Space Pirate Command Ships, and the assistants eyes turned to spot a heavily diminished force.

"Sir, it looks as if the Pirates are running out of troops." the assistant declared as he averted his eyes from the window.

"Excellent." Baxter said happily. "Now we can begin to start planning to get the Pirates out of the way."

******

The Space Pirate Command Cruiser was losing its troops at an incredible rate. Kraid had been dispatched to capture Samus, and had not yet returned. Waiting constantly below the ship, some of the Pirates looked out of the upper window, trying to catch a glimpse of Kraid or Samus. The Pirate Commanders though, were growing nervous. Kraid had to be successful, otherwise it would be their heads on the chopping block.

"I have detected Kraid falling directly above the ship's upper hatch." one stated.

The Space Pirates standing around the ship looking run back to their posts to avoid missing anything.

"Opening the upper hatch." another responded.

Kraid fell through the upper hatch, landing heavily on the floor. He tried to get to his feet, but couldn't manage it. The look of agony on his face revealed all to the Commanders.

"Samus has escaped our grasp yet again. Vulcan will not be pleased." Kraid stumbled.

"We have worse news. The Federation scum have beaten us back. Reinforcements are nearly depleted."

"Call a retreat." Kraid demanded. "If we cut our losses maybe Vulcan will show mercy."

"Yes, sir." a Commander replied.

The ship turned around into the depths of space in defeat, followed by the rest of the fleet. The G.F.S. Olympus still flew gloriously through space, the Space Pirates had left only a minor dent. The Space Pirates had rendered themselves visible to the Federation again; the remainder of the Space Pirate Operations had to remain covert if they were to go without major Federation interference.

******

Samus' ship landed on Tallon IV; hyperdrive carried her there in minutes.

"Good luck, lady." Adam called as Samus exited the ship. Samus stopped to admire the view; the Tallon Overworld was as beautiful as it was before the Leviathan Impact ruined the planet, corrupting it with Phazon. According to Samus' logbook, the impact was set to turn the entire planet into a 'barren, Class XIII wasteland'.

A waterfall poured water into a freely flowing, crystal clear river now teeming with life. Samus' eyes followed the flow of the river to the Artifact Temple, a Chozo building constructed over the Leviathan Impact Crater to stop Metroid Prime from destroying the planet. Samus marvelled at the colourful flora beside the river, and the dense trees where the soil was once infertile; the Tallon Overworld was a jungle once more. In fact, it was practically a new world to Samus, who had never seen the planet without the presence of Phazon.

Samus leapt over the river and headed towards the door leading to a cavern which in turn lead to the Chozo Ruins. Samus shot her Power beam at the door and ran through it, walking right in front of a Beetle. Samus quickly fired a shot at it, failing to finish it off. Samus thought that it was any wonder an entire Federation Cruiser's crew were unable to fend off an invasion from an evil race of creatures called the Ing on Aether; their weaponry was weak. The Federation clearly thought that each troopers life was expendable, something that truly repulsed Samus. Samus launched a few more shots into the Beetle, and finally killed it.

Samus walked through another few doors to arrive at the Chozo Ruins. Samus paused to admire the ruins, though very little had changed since she departed the planet. The only new thing of note were some grasses thinly covering some areas. Samus soon got over the changed surroundings to set about regaining her lost abilities; she would need them to stop the Federation's wild plan and rescue the galaxy, a concept she was all too familiar with.

**Chapter 6 a few days after the New Year. Until then, happy 2009!**


	6. A Successful Failure

His battle with Samus was the furthest thing from Kraid's mind. In the Medical Wing of the Space Pirate Cruiser he was instead trying to shut out the intense pain of crude Space Pirates scissors and scalpels removing dead flesh from where Samus' Power Beam had struck his under developed hide. Even the anaesthetic couldn't quell the pain. Kraid cringed with every blade and needle forcefully pushed into his wounds, vowing in his head to take swift revenge on Samus Aran.

After what felt like many agonising hours of jabbing and cutting, Kraid's surgery was complete, his wounds stitched up, looking barely different than he did before the fight. Kraid walked into the cockpit of the ship, his body still aching from his ordeal. He saw the Space Pirate Homeworld ahead in full view. He would have to face Vulcan soon, but his thoughts couldn't afford to turn to death, as the one thing Vulcan hated as Commander was defeatism. Though Kraid thought if Vulcan really wanted him dead, then he wouldn't have allowed the Medical Team to assist him. Still, he had better not think about that either. Vulcan despised cockiness.

As the ship entered the Homeworld's Upper Atmosphere, Kraid began to think about what he could do to capture Samus after he reprepared. The Space Pirates had probes around all planets Samus had visited previously; if Samus made planetfall anywhere she had been before, the Space Pirates would know about it. Kraid could keep persisting until he became fully grown and would surely eventually capture her. That is, if Vulcan would allow it.

******

Adam lay in wait for Samus inside the ship, running routine scans on the area surrounding Tallon IV. The ship was empty, and Samus hadn't made contact to him since she left for the Chozo Ruins. The Etecoons and Dachoras Samus had rescued three months ago during her time on the BSL were placed in the ships' Stasis Tanks. Understandably so, as they couldn't care for them while on the run, though when Adam was alone he often wished for the company.

Adam ran another routine scan to check for threats, analysing the space around Tallon IV, checking for signals tracking the ship, as well as the conditions of the planet and it's atmosphere. Adam waited for the results eagerly. Minutes later, the results started to arrive.

"_No abnormalities detected on planet's surface."_ Adam was slightly relieved.

"_No interstellar objects on course for the planet." _Okay.

"_Electro-magnetic interference minimal." _Another good result.

"_Multiple radio signals detected tracing the ship."_ Adam's computerised 'heart' sank.

Adam quickly checked the details of the report:

"_Two radio signals have been detected tracing the ships radio frequency. One is confirmed to be of Space Pirate origin; the other of Federation technology. Back tracing revealed that the Space Pirate ship is an unmanned tracking pod orbiting the planet, and that the Federation ship is another Hunter-Class Gunship with similar capabilities to this ship. Registration is classified, as is access to any other details about the ship. Recommended actions are to destroy the Space Pirate Probe and scramble the signal from the ship to prevent further tracking from the Federation vessel; if approach towards ships position occurs, destroy the Federation ship."_

Shocked that anyone would be tracking them at all, Adam decided to follow the given advice. The Space Pirate Probe would likely be transmitting back to the Space Pirate Homeworld at any moment, and destroying the Federation ship with no need would achieve nothing but drawing Federation attention to their position. He locked the Ship's Missile Launcher on to the Space Pirate Pod's Heat Signature and fired, then scrambled the ship's signal to throw the Federation ship off.

Adam had detected no approach from the Federation ship, and that the missile had hit and destroyed its target, and he knew he had narrowly averted the crisis.

******

The dark green ship cruised past Tallon IV lazily, as if trying to find something. Inside the ship, the occupant was hard at work at the ship's computer.

"Do we have any details on the signal we're tracking?" asked a voice inside.

"Very few." replied the feminine voice of the ships computer. "We know that the ship is a Federation vessel, but all other details are classified. I'm trying to negotiate the firewall for a few more details but it seems a- oh... I've lost the signal."

"Strange." the voice said calmly. "Maybe a mechanical flaw."

"Possibly." the computer stated bluntly. "I suggest we continue on our mission."

"I agree. Continue on our previous flight path." the pilot commanded.

With these words, the ship took off speedily away from Tallon IV.

******

The Space Pirate ship landed cleanly on the Landing Pad on the Space Pirate Homeworld, and Kraid exited, shielded from the corrosive acid rain constantly falling on the planet by a protective film coating his body. He walked slowly towards the nearby Command Complex to confront Vulcan, now feeling a lot less residual pain from his operation. Kraid was nervous, but he daren't show it. He had to put his best foot forward if he were to avoid an unfortunate ending.

Kraid entered the building and walked toward Vulcan's Command Centre. The door opened, and Kraid walked nervously through.

"Kraid." Vulcan said as he turned from his Command Computer to face him. "You have miserably failed your mission. That disappoints me."

Kraid was relieved Vulcan hadn't exploded with rage yet, but he had a long way to go.

"Samus...was too good." Kraid admitted, almost accepting the fact himself.

"It appears that Samus was a more formidable foe than I thought." Vulcan conceded. "I underestimated her. My apologies."

"I'm spared?" Kraid asked in amazement.

"Kraid, why should you pay for my mistake." Vulcan answered. "Go back to your Accelerated Development Chamber for a while, and then you can try facing Samus again."

Kraid was astonished; Vulcan had not only spared his life, but not shown a hint of anger as well. Kraid knew this compassion was slightly suspect, but he was so grateful that he just went off as Vulcan asked, not bothering to try and make Vulcan reveal his motive. Revenge would have to wait. Vulcan waited until Kraid had well and truly left before asking a Space Pirate to enter the room.

"Did you remove the sample during the surgery?" Vulcan asked the Pirate.

"Extraction was successful." came the reply. "The samples are being taken to Research and Production as we speak."

"Excellent work." Vulcan congratulated. "All is going according to plan. All we need to do is keep the Federation distracted for long enough and we will be done. Though that presents a bit of a challenge..."

"Uh, another thing." the Pirate interrupted. "The Probe orbiting Tallon IV has been destroyed after detecting a Federation ship."

"Excellent!" Vulcan cried. "This could be the distraction we need. If we intercept the Federation vessel they will send troops to engage us, but we will have left, leaving a few clues on the planet's surface, and they will be on a wild goosechase on Tallon IV for long enough to complete our mission. We must send a small force there immediately."

"Who do you propose to lead this force." the Pirate asked.

"I will head this operation." Vulcan answered. "and I will take a Commando Unit and some Aerotroopers."

"Sounds like a plan." the Pirate stated. "The only thing to do now is to execute it."

"Well," Vulcan called. "What are we waiting for?"


	7. The Ruins Rediscovery

Samus walked back into the main room of the Chozo Ruins. She had adventured through all of the caverns and corners of the complex tunnels of the ruins, recovering every ability she found along the way. She had currently restored her Morph Ball, Bombs, her usual, stronger Missiles, the Varia Suit, several Energy Tanks and Missile Expansions; even the Ice Beam. Samus was unsure how exactly the Federation managed to emulate the suit she absorbed after defeating the SA-X, an X parasite mimicking her, as the Metroid Vaccine used to cure her X Infection left her vulnerable to cold, but whatever they did, she could now use her Ice Beam harmlessly.

Samus had also began to reconstruct her logbook, she had regained her scans of Zoomers, Geemers, Beetles, various kinds of War Wasps, Tangleweed, as well as all sorts of Chozo Lore and Architecture. Samus had basically everything in the ruins and the Tallon Overworld scanned and recorded to her log book.

Samus walked towards the door leading to the Tallon Overworld and her ship. She felt there was no need to explore the other areas of Tallon IV, she didn't need to restore too many more of her abilities, the only one she might miss that could be found on this planet would be Power Bombs, Hi-Jump and Screw Attack were nowhere to be found on Tallon IV, and the Space Jump found here was right found in a room right behind her ship, though it didn't provide quite the same effect; it only provided a small mid-air boost compared to the infinite jump the other, more advanced Space Jump provided.

Samus was about to shoot the door in front of her when she heard a loud screech and and saw sand fly into her visor as she turned to look at the source. Samus cleared her visor with her hand, and spotted an Plated Beetle emerged from the sand. Before Samus could run for the door, the creature blocked her escape route. Samus quickly scanned it, and waited for it to charge as it strafed from side to side. Plated Beetles could only be damaged by striking them in the back, where their armour couldn't protect them, so allowing it to charge was the only way to defeat it. It soon charged head on at Samus, who jumped out of the way, and fired a missile at its exposed back. It hit the creature's hindquarters directly, throwing it straight forward into the wall in front of it. The Plated Beetle fell to the ground, and no sooner leapt to its feet angrily. It charged again furiously at Samus, who rolled to the right and fired another missile at its back. The Beetle was hit again, and this time it destroyed the armour, which cracked around it and fell to pieces. Samus charged an Ice Beam shot, and unloaded it into the creature, freezing it, and then used another missile to shatter it, finishing it off.

Samus collected the Missile Ammunition the Beetle dropped, and turned towards the door. Before she could leave, Samus heard a loud cracking sound to her left, where the creature had collided with the wall. She turned to investigate as the wall began to crumble and fall apart. Samus almost thought the ruins were falling apart around her, but the wall stopped breaking past the initial impact area. Samus was half relieved as the dust from the falling stones started to subside. Samus watched as the dust cleared, revealing a door that was once hidden by the wall. Samus had never seen this before on her previous adventure here.

Surprised, Samus shot the door and ran through, arm cannon raised in case of hostility inside. All Samus saw was a small, circular room with pillars lining a large inner circle, as if a centrepiece was once there. Looking around further in the room, Samus discovered two glowing panels; these indicated Chozo Lore around the ruins, so Samus readied her Scan Visor.

Surely enough, they were lore scans; Samus aimed her Scan Visor at a panel, and viewed the scan results:

"_After the revival, the surviving Chozo set about analysing the damage that had occurred during the Period of Haze. The few remaining Chozo decided to investigate the environments of the planet to analyse what had changed in our precious homeworld. The results were atrocious. The mountains of the Phendrana Drifts had Laboraties carved into the beautiful rockface, and the pristine jungle overworld had been desecrated with the wreckage of a large interstellar object. But the worst was yet to come. Further into the homeworld, a mine was discovered,with a drill leading directly to the Artifact Temple; surely the operaters of this mine had been mining the Great Poison. With this foul discovery in mind, the remaining elders made the decision to leave the planet; we needed to go to another known Chozo world, and our elders decided on Zebes."_

Samus thought about this carefully. What could the revival be? To find out, Samus scanned the second, and last panel.

"_To set about getting Zebes the elders proposed we build a vessel to take us to Zebes. A new section was erected off the main room of the ruins of our society, which we would seal off after we were finished, so those that ruined our homeland would be oblivious to our actions. The prophets__ declared that our construction would one day be discovered by the same 'Chosen One' who saved the planet from the Great Poison during the in Period of Haze. The operation was successful, and, years later, the area was sealed, knowing that only the worthy would ever see it, and prepared to leave the next year. However, our astromers witnessed a large explosion within the area of Zebes, and we were forced to depart prematurely to investigate, for the good of our people, and our operation."_

Samus wondered about what this lore meant. When Samus first arrived on Tallon IV, the Laboraties and Mine were there, and that was when the only Chozo occupying the ruins were the Chozo Ghosts, Chozo corrupted by Phazon. Then something inside Samus clicked, and she realised what the 'Period of Haze' was. When the Chozo were corrupted their judgement was clouded, hence the 'Haze', and lurked around certain areas of the ruins mindlessly. They were then 'revived'; the Phazon corruption cured after the destruction of all Phazon, thanks to Samus' actions on Phaaze, the source of Phazon, and the events stated in the lore occurred. The explosion on Zebes was when Samus destroyed Zebes after taking out the Space Pirate Base there, triggering the planetary self-destruct system. The Chozo were on a hopeless mission.

Samus then left back for her ship; there was nothing no more to see, and it was clear see had to make a decision; the Chozo, the people that took her in, and made her who she was today, were still alive, but the Federation posed a major direct threat to her welfare, as well as the rest of the cosmos.

****** 

Jonathan Baxter had the Federation Staff onboard the GFS Olympus hard at work. The researchers had detected a major energy disturbance around the location Zebes once was, and dispatched a Bounty Hunter to investigate. Since this was relevant to their current research, they had to find out what was happening, an energy rift could potentially ruin the plan to take over the things beyond physical existance should anyone settle in first.

Baxter was restless; the Development Team had already created and polished the technology to open 'portals' beyond the physical world, all they were waiting on was the tests to show that it was safe for transport, and the 'revolution' could go ahead. Baxter was off in a world of his own, and missed his assistant entering the room.

"Sir." the assistant started.

"What?" Baxted asked impatiently, his train of thought interrupted.

"The energy disturbance is confirmed to be a portal, according to our bounty hunters reports." the assistant answered.

"Looks like we will have to combat someone, or something upon entry." Baxter said. "What a shame. We will have to use force."

"The report also indicates that the Space Pirates aren't involved at all." the assistant stated. "So using force is most likely uneccessary."

"You miss the point." Baxter said bluntly. "There will be no rules beyond this world. No law, no authority. We can do whatever we like until we enforce our own rules. All we need is the Space Pirates out of the way and we are in clear. The Federation will control everything in the cosmos, using energy itself to fuel their operations, and, best of all, even the Federation Council have approved of the operation."

"Shall we call a truce?" the assistant asked.

"Yes... perfect." Baxter responded. "Prepare it now. That will keep them at bay until we can use our new technology to eliminate the threat once and for all."

"I shall start work immediately." the assistant declared as he left the room.

Baxter realised that the Federation was drawing ever closer to the objective of using the world of energy to control outside territories. Soon the Federation would be able to take over every system known to the Federation, plus more, and go unopposed throughout the many universes, taking over by force if needed. Baxter had always craved that kind of power, and this thought made Baxter both excited, and anxious. Soon, he would have to report to his superiors at Daiban, the Federation Capital, and explain why his mission was way behind schedule, and its current progress, knowing that a poor showing could result in him missing out on the spoils once the mission was complete. He would need to do everything perfectly, or risk losing everything he had been working for, and more...

**Glad I managed to finish another chapter. The next one will take a little longer (About half a week.) to write, as I will be on holiday at Phillip Island. Maybe some fellow Australians might know where that is, but I seriously doubt anyone else would. Anyway, in the meantime, enjoy this chapter, and, if you have any comments, questions or critisms, don't hesitate to leave a review or send me a message, and I will get back to you after I get back. **


End file.
